I discovered Mendeley today. Except for it's citation organization features, for which it is not unique (there are CiteUlike, JabRef and more) it works as a desktop app that indexes all your local PDF documents, and has an internal PDF viewer that lets you annotate the documents. These two are killer features that I've been looking for since a long time.
It's a pity though that it is proprietary. It would naturally feel better to put your work in the hands of an open system. Interesting then to find gPapers which seems to have similar goals on the app side. Hoping it will mature fast so it can replace the inevitable need for something like mendeley with an open solution (Currently I can't open the documents individually, for full screen reading and annotation. Maybe it's just a problem in Ubuntu 9.04?). So, if you have left over spare time, and know python, please go make this app beat mendeley! :)
Installation on Ubuntu Jaunty (9.04) was not 100% according to the instructions on the website, so I've compiled an instruction that works:
sudo apt-get install python python-glade2 python-gnome2 python-sqlite graphviz
( python-sqlite3 is changed for python-sqlite for Ubuntu 9.04 )
Now run (from wherever you want to install to):
svn checkout http://gpapers.googlecode.com/svn/trunk/ gpapers
tar -zvxf ext/Django-1.0.2-final.tar.gz Django-1.0.2-final/django
mv Django-1.0.2-final/django .
sudo apt-get install python-poppler